Skip to content

More docs #1291

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
David-Baddeley merged 6 commits into from
Oct 12, 2022
Merged

More docs #1291

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
06b011d
doc updates (most of #1289)
David-Baddeley Oct 3, 2022
06b05c5
fix numbering
David-Baddeley Oct 4, 2022
aed10e3
more cluster docs
David-Baddeley Oct 4, 2022
8132344
more compute docs
David-Baddeley Oct 4, 2022
278ef1a
temporary hack to stop density mapping causing a segfault
David-Baddeley Oct 4, 2022
9884aef
added localisation rule example
David-Baddeley Oct 5, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 11 additions & 5 deletions PYME/recipes/localisations.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -97,14 +97,20 @@ def execute(self, namespace):

renderer = renderers.RENDERERS[str(self.renderingModule)](None, cf)

namespace[self.outputImage] = renderer.Generate(self.trait_get())
logger.debug('about to generate')

out = renderer.Generate(self.trait_get())

logger.debug(f'generated:{out.data_xyztc.shape}')

namespace[self.outputImage] = out

def _view_items(self, params=None):
from traitsui.api import Group, Item
return [Item('renderingModule'),
Item('pixelSize'),
Item('colours', style='text'),#editor=CSVListEditor()),
Item('softRender'),
#Item('colours', style='text'),#editor=CSVListEditor()),
#Item('softRender'),
Group(
Item('jitterVariable'),
Item('jitterScale'),
Expand All @@ -116,11 +122,11 @@ def _view_items(self, params=None):
Group(
Item('zSliceThickness'),
Item('zBoundsMode'),
Item('zBounds', visible_when='zBoundsMode=="manual"'),
#Item('zBounds', visible_when='zBoundsMode=="manual"'),
label='3D', visible_when='"3D" in renderingModule'),
Group(
Item('xyBoundsMode'),
Item('manualXYBounds', visible_when='xyBoundsMode=="manual"'),
#Item('manualXYBounds', visible_when='xyBoundsMode=="manual"'),
label='Output Image Size',
),
]
Expand Down
16 changes: 16 additions & 0 deletions docs/cluster/PYMECluster.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,22 @@
The PYME Storage and compute cluster architecture
*************************************************

The PYME cluster architecture facilitates scalable parallelized data analysis and
distributed data storage, and can operate either on a cluster or (when performance
requirements are more modest) on a single computer. It is designed to allow easy
scaling to larger cluster sizes in the future (i.e. you can start with a single node
and add more as needed).

It consists of two key components:
- a distributed storage component.
- a distributed analysis component which is data-locality aware.

In addition there is a web-based user interface to the components.

Whilst the storage and analysis components can be used separately, the best results are
obtained when they are used together such that the data-locality features of the analysis
scheduling can be used.


.. toctree::
:maxdepth: 1
Expand Down
Loading